Coevolution analysis of protein residues
Getting started
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Installation guide
API
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Data
Reference sequence ID:
Multiple sequence alignment:
Download from Pfam
Pfam ID:
Upload files
MSA:
Tree:
(required for tree-based seq. weighting only)
Coevolution score function
Correlation-based methods
Change matrix:
Control
McLachlan
Volume change
Absolute volume change
pI change
Absolute pI change
Hydropathy index change
Absolute hydropathy index change
Correlation function:
Pearson
Spearman
Case analysis
Case analysis with conservation normalization
ELSC
Mutual information
Normalization:
none
min{H(X|Y),H(Y|X)}
min{H(X),H(Y)}
max{H(X|Y),H(Y|X)}
max{H(X),H(Y)}
H(X)+H(Y)
H(X,Y)
Chi-square
Quartets
Coevolution score analysis
Analyze coevolution scores
Protein structure:
Download from PDB
PDB ID:
Upload file
Structure file:
Interaction threshold:
Angstrom
Distance-score plot:
Yes
No
ROC curve:
Yes
No
Task submission
Email address:
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Sequence filtering
Maximum fraction of gaps per sequence:
Maximum similarity between two sequences (0-1):
Minimum number of sequences after filtering:
Site filtering
Maximum fraction of gaps per site:
Maximum fraction of sequences having the same residue/group:
Site pair filtering
Minimum separation between sites (0 = adjacent ok):
Maximum fraction of sequences in connected gaps:
Additional data preprocessing
Residue grouping:
None
Elcock and McCammon, PNAS 2001
Guharoy and Chakrabarti, PNAS 2005
Sequence weighting:
None
Tree based
Random walk based
Gap handling:
As noise
As signal